Untitled

No description

Report generated at 2020-05-04 14:44:59

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	188255058	177519184
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	127559443	172494915
Mapped(QC-failed)	0	0
% Mapped	67.7600	97.1700
Paired	188255058	177519184
Paired(QC-failed)	0	0
Read1	94127529	88759592
Read1(QC-failed)	0	0
Read2	94127529	88759592
Read2(QC-failed)	0	0
Properly Paired	125019986	168093297
Properly Paired(QC-failed)	0	0
% Properly Paired	66.4100	94.6900
With itself	125985758	170816950
With itself(QC-failed)	0	0
Singletons	1573685	1677965
Singletons(QC-failed)	0	0
% Singleton	0.8400	0.9500
Diff. Chroms	301005	1509587
Diff. Chroms (QC-failed)	0	0

Marking duplicates (filtered BAM)

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

	rep1	ctl1
Unpaired Reads	0	0
Paired Reads	55914622	73622728
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	515874	559519
Paired Opt. Dupes	1951	3080
% Dupes/100	0.0092	0.0076

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	55907862	73528740
Distinct Read Pairs	55392066	72972791
One Read Pair	54881461	72421080
Two Read Pairs	505567	547586
NRF = Distinct/Total	0.9908	0.9924
PBC1 = OnePair/Distinct	0.9908	0.9924
PBC2 = OnePair/TwoPair	108.5543	132.2552

Mitochondrial reads are filtered out.

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally

0-0.5 is severe bottlenecking
0.5-0.8 is moderate bottlenecking
0.8-0.9 is mild bottlenecking
0.9-1.0 is no bottlenecking

Flagstat (filtered/deduped BAM)

Filtered and duplicates removed

	rep1	ctl1
Total	110797496	146126418
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	110797496	146126418
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	110797496	146126418
Paired(QC-failed)	0	0
Read1	55398748	73063209
Read1(QC-failed)	0	0
Read2	55398748	73063209
Read2(QC-failed)	0	0
Properly Paired	110797496	146126418
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	110797496	146126418
With itself(QC-failed)	0	0
Singletons	0	0
Singletons(QC-failed)	0	0
% Singleton	0.0000	0.0000
Diff. Chroms	0	0
Diff. Chroms (QC-failed)	0	0

Peak calling

Reproducibility QC and peak detection statistics

The number of peaks is capped at 300K for peak-caller MACS2

	overlap
Nt	0
N1	269886
Np	0
N optimal	269886
N conservative	269886
Optimal Set	rep1-pr
Conservative Set	rep1-pr
Rescue Ratio	0.0000
Self Consistency Ratio	1.0000
Reproducibility	pass

Overlapping peaks

N1: Replicate 1 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Nt: True Replicate consisten overlapping peaks (comparing true replicates Rep1 vs Rep2 )
Np: Pooled-pseudoreplicate consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2 )
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'

Enrichment

Strand cross-correlation measures

Performed on subsampled reads (15M)

	rep1
Reads	15000000
Est. Fragment Len.	105
Corr. Est. Fragment Len.	0.1936
Phantom Peak	50
Corr. Phantom Peak	0.2246
Argmin. Corr.	1500
Min. Corr.	0.1757
NSC	1.1019
RSC	0.3662

NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.

Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value

Fraction of reads in overlapping peaks

	rep1-pr
Fraction of Reads in Peak	0.3535

ppr: Overlapping peaks comparing pooled pseudo replicates
rep1-pr: Overlapping peaks comparing pseudoreplicates from replicate 1
rep2-pr: Overlapping peaks comparing pseudoreplicates from replicate 2
repi-repj: Overlapping peaks comparing true replicates (rep i vs. rep j)

Other quality metrics

Fingerprint and Jensen-Shannon distance

	rep1
% genome enriched	0.1837
AUC	0.4961
CHANCE divergence	0.1557
Elbow Point	0.0000
JS Distance	0.7072
Synthetic AUC	0.5004
Synthetic Elbow Point	0.1982
Synthetic JS Distance	0.4306